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Deng TX, Ma XY, Duan A, Lu XR, Abdel-Shafy H. Genome-wide copy number variant analysis reveals candidate genes associated with milk production traits in water buffalo (Bubalus bubalis). J Dairy Sci 2024; 107:7022-7037. [PMID: 38762109 DOI: 10.3168/jds.2023-24614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 03/28/2024] [Indexed: 05/20/2024]
Abstract
Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variants (CNV) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 CNV regions (CNVR), with 1,993 shared CNVR being found within the studied buffalo types. Analyzing CNVR highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst-based population differentiation, revealing 11 genes within CNVR that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci analysis revealed differentially expressed CNVR-derived genes (DECG) associated with milk production traits. Notably, known milk production-related genes were among these DECG, validating their relevance. Last, a GWAS identified 3 CNVR significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species.
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Affiliation(s)
- Ting-Xian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
| | - Xiao-Ya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Anqin Duan
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Xing-Rong Lu
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Hamdy Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613, Giza, Egypt
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2
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Chen D, Chitre AS, Nguyen KMH, Cohen K, Peng B, Ziegler KS, Okamoto F, Lin B, Johnson BB, Sanches TM, Cheng R, Polesskaya O, Palmer AA. A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603984. [PMID: 39071405 PMCID: PMC11275765 DOI: 10.1101/2024.07.17.603984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Affordable sequencing and genotyping methods are essential for large scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, non-human model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping-by-sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping-by-sequencing and more recently generated by low-coverage whole-genome-sequencing data. Using double-digest genotyping-by-sequencing data from 5,745 heterogeneous stock rats (mean 0.21x coverage) and low-coverage whole-genome-sequencing data from 8,760 heterogeneous stock rats (mean 0.27x coverage), we can impute 7.32 million bi-allelic single-nucleotide polymorphisms with a concordance rate >99.76% compared to high-coverage (mean 33.26x coverage) whole-genome sequencing data for a subset of the same individuals. Our results demonstrate the feasibility of using sequencing data from double-digest genotyping-by-sequencing or low-coverage whole-genome-sequencing for accurate genotyping, and demonstrate techniques that may also be useful for other genetic studies in non-human subjects.
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Affiliation(s)
- Denghui Chen
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Apurva S. Chitre
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Khai-Minh H. Nguyen
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Katarina Cohen
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Beverly Peng
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Kendra S. Ziegler
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Faith Okamoto
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Bonnie Lin
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Benjamin B. Johnson
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Thiago M. Sanches
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
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Han Z, Yang C, He H, Huang T, Yin Q, Tian G, Wu Y, Hu W, Lu L, Bajpai AK, Mi J, Xu F. Systems Genetics Analyses Reveals Key Genes Related to Behavioral Traits in the Striatum of CFW Mice. J Neurosci 2024; 44:e0252242024. [PMID: 38777602 PMCID: PMC11211725 DOI: 10.1523/jneurosci.0252-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
The striatum plays a central role in directing many complex behaviors ranging from motor control to action choice and reward learning. In our study, we used 55 male CFW mice with rapid decay linkage disequilibrium to systematically mine the striatum-related behavioral functional genes by analyzing their striatal transcriptomes and 79 measured behavioral phenotypic data. By constructing a gene coexpression network, we clustered the genes into 13 modules, with most of them being positively correlated with motor traits. Based on functional annotations as well as Fisher's exact and hypergeometric distribution tests, brown and magenta modules were identified as core modules. They were significantly enriched for striatal-related functional genes. Subsequent Mendelian randomization analysis verified the causal relationship between the core modules and dyskinesia. Through the intramodular gene connectivity analysis, Adcy5 and Kcnma1 were identified as brown and magenta module hub genes, respectively. Knock outs of both Adcy5 and Kcnma1 lead to motor dysfunction in mice, and KCNMA1 acts as a risk gene for schizophrenia and smoking addiction in humans. We also evaluated the cellular composition of each module and identified oligodendrocytes in the striatum to have a positive role in motor regulation.
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Affiliation(s)
- Zhe Han
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Chunhua Yang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Hongjie He
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Tingting Huang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Quanting Yin
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Geng Tian
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Yuyong Wu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
| | - Wei Hu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Akhilesh Kumar Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Jia Mi
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Fuyi Xu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
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Kuhn BN, Cannella N, Chitre AS, Nguyen KMH, Cohen K, Chen D, Peng B, Ziegler KS, Lin B, Johnson BB, Missfeldt Sanches T, Crow AD, Lunerti V, Gupta A, Dereschewitz E, Soverchia L, Hopkins JL, Roberts AT, Ubaldi M, Abdulmalek S, Kinen A, Hardiman G, Chung D, Polesskaya O, Solberg Woods LC, Ciccocioppo R, Kalivas PW, Palmer AA. Genome-wide association study reveals multiple loci for nociception and opioid consumption behaviors associated with heroin vulnerability in outbred rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582340. [PMID: 38712202 PMCID: PMC11071306 DOI: 10.1101/2024.02.27.582340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The increased prevalence of opioid use disorder (OUD) makes it imperative to disentangle the biological mechanisms contributing to individual differences in OUD vulnerability. OUD shows strong heritability, however genetic variants contributing toward vulnerability remain poorly defined. We performed a genome-wide association study using over 850 male and female heterogeneous stock (HS) rats to identify genes underlying behaviors associated with OUD such as nociception, as well as heroin-taking, extinction and seeking behaviors. By using an animal model of OUD, we were able to identify genetic variants associated with distinct OUD behaviors while maintaining a uniform environment, an experimental design not easily achieved in humans. Furthermore, we used a novel non-linear network-based clustering approach to characterize rats based on OUD vulnerability to assess genetic variants associated with OUD susceptibility. Our findings confirm the heritability of several OUD-like behaviors, including OUD susceptibility. Additionally, several genetic variants associated with nociceptive threshold prior to heroin experience, heroin consumption, escalation of intake, and motivation to obtain heroin were identified. Tom1 , a microglial component, was implicated for nociception. Several genes involved in dopaminergic signaling, neuroplasticity and substance use disorders, including Brwd1 , Pcp4, Phb1l2 and Mmp15 were implicated for the heroin traits. Additionally, an OUD vulnerable phenotype was associated with genetic variants for consumption and break point, suggesting a specific genetic contribution for OUD-like traits contributing to vulnerability. Together, these findings identify novel genetic markers related to the susceptibility to OUD-relevant behaviors in HS rats.
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Polesskaya O, Boussaty E, Cheng R, Lamonte O, Zhou T, Du E, Sanches TM, Nguyen KM, Okamoto M, Palmer AA, Friedman R. Genome-wide association study for age-related hearing loss in CFW mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598304. [PMID: 38915500 PMCID: PMC11195089 DOI: 10.1101/2024.06.10.598304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Age-related hearing impairment is the most common cause of hearing loss and is one of the most prevalent conditions affecting the elderly globally. It is influenced by a combination of environmental and genetic factors. The mouse and human inner ears are functionally and genetically homologous. Investigating the genetic basis of age-related hearing loss (ARHL) in an outbred mouse model may lead to a better understanding of the molecular mechanisms of this condition. We used Carworth Farms White (CFW) outbred mice, because they are genetically diverse and exhibit variation in the onset and severity of ARHL. The goal of this study was to identify genetic loci involved in regulating ARHL. Hearing at a range of frequencies was measured using Auditory Brainstem Response (ABR) thresholds in 946 male and female CFW mice at the age of 1, 6, and 10 months. We obtained genotypes at 4.18 million single nucleotide polymorphisms (SNP) using low-coverage (mean coverage 0.27x) whole-genome sequencing followed by imputation using STITCH. To determine the accuracy of the genotypes we sequenced 8 samples at >30x coverage and used calls from those samples to estimate the discordance rate, which was 0.45%. We performed genetic analysis for the ABR thresholds for each frequency at each age, and for the time of onset of deafness for each frequency. The SNP heritability ranged from 0 to 42% for different traits. Genome-wide association analysis identified several regions associated with ARHL that contained potential candidate genes, including Dnah11, Rapgef5, Cpne4, Prkag2, and Nek11. We confirmed, using functional study, that Prkag2 deficiency causes age-related hearing loss at high frequency in mice; this makes Prkag2 a candidate gene for further studies. This work helps to identify genetic risk factors for ARHL and to define novel therapeutic targets for the treatment and prevention of ARHL.
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Affiliation(s)
- Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ely Boussaty
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivia Lamonte
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Thomas Zhou
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Eric Du
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mika Okamoto
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rick Friedman
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
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Teng J, Zhai T, Zhang X, Zhao C, Wang W, Tang H, Wang D, Shang Y, Ning C, Zhang Q. Improving multi-population genomic prediction accuracy using multi-trait GBLUP models which incorporate global or local genetic correlation information. Brief Bioinform 2024; 25:bbae276. [PMID: 38856170 PMCID: PMC11163384 DOI: 10.1093/bib/bbae276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/05/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024] Open
Abstract
In the application of genomic prediction, a situation often faced is that there are multiple populations in which genomic prediction (GP) need to be conducted. A common way to handle the multi-population GP is simply to combine the multiple populations into a single population. However, since these populations may be subject to different environments, there may exist genotype-environment interactions which may affect the accuracy of genomic prediction. In this study, we demonstrated that multi-trait genomic best linear unbiased prediction (MTGBLUP) can be used for multi-population genomic prediction, whereby the performances of a trait in different populations are regarded as different traits, and thus multi-population prediction is regarded as multi-trait prediction by employing the between-population genetic correlation. Using real datasets, we proved that MTGBLUP outperformed the conventional multi-population model that simply combines different populations together. We further proposed that MTGBLUP can be improved by partitioning the global between-population genetic correlation into local genetic correlations (LGC). We suggested two LGC models, LGC-model-1 and LGC-model-2, which partition the genome into regions with and without significant LGC (LGC-model-1) or regions with and without strong LGC (LGC-model-2). In analysis of real datasets, we demonstrated that the LGC models could increase universally the prediction accuracy and the relative improvement over MTGBLUP reached up to 163.86% (25.64% on average).
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Affiliation(s)
- Jun Teng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China
- Shandong Futeng Food Co. Ltd., Zaozhuang 277500, Shandong, China
| | - Tingting Zhai
- National Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xinyi Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Changheng Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Wenwen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Hui Tang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Dan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yingli Shang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Chao Ning
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, Shandong, China
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Lekkos K, Bhuiyan AA, Albloshi AMK, Brooks PM, Coate TM, Lionikas A. Validation of positional candidates Rps6ka6 and Pou3f4 for a locus associated with skeletal muscle mass variability. G3 (BETHESDA, MD.) 2024; 14:jkae046. [PMID: 38577978 PMCID: PMC11075558 DOI: 10.1093/g3journal/jkae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/17/2024] [Indexed: 04/06/2024]
Abstract
Genetic variability significantly contributes to individual differences in skeletal muscle mass; however, the specific genes involved in that process remain elusive. In this study, we examined the role of positional candidates, Rps6ka6 and Pou3f4, of a chromosome X locus, implicated in muscle mass variability in CFW laboratory mice. Histology of hindlimb muscles was studied in CFW male mice carrying the muscle "increasing" allele C (n = 15) or "decreasing" allele T (n = 15) at the peak marker of the locus, rs31308852, and in the Pou3f4y/- and their wild-type male littermates. To study the role of the Rps6ka6 gene, we deleted exon 7 (Rps6ka6-ΔE7) using clustered regularly interspaced palindromic repeats-Cas9 based method in H2Kb myogenic cells creating a severely truncated RSK4 protein. We then tested whether that mutation affected myoblast proliferation, migration, and/or differentiation. The extensor digitorum longus muscle was 7% larger (P < 0.0001) due to 10% more muscle fibers (P = 0.0176) in the carriers of the "increasing" compared with the "decreasing" CFW allele. The number of fibers was reduced by 15% (P = 0.0268) in the slow-twitch soleus but not in the fast-twitch extensor digitorum longus (P = 0.2947) of Pou3f4y/- mice. The proliferation and migration did not differ between the Rps6ka6-ΔE7 and wild-type H2Kb myoblasts. However, indices of differentiation (myosin expression, P < 0.0001; size of myosin-expressing cells, P < 0.0001; and fusion index, P = 0.0013) were significantly reduced in Rps6ka6-ΔE7 cells. This study suggests that the effect of the X chromosome locus on muscle fiber numbers in the fast-twitch extensor digitorum longus is mediated by the Rps6ka6 gene, whereas the Pou3f4 gene affects fiber number in slow-twitch soleus.
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Affiliation(s)
- Konstantinos Lekkos
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Afra A Bhuiyan
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Abdullah M K Albloshi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
- Department of Anatomy and Histology, School of Medicine, University of Albaha, Alaqiq 65779, Saudi Arabia
| | - Paige M Brooks
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Thomas M Coate
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
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King CP, Chitre AS, Leal-Gutiérrez JD, Tripi JA, Hughson AR, Horvath AP, Lamparelli AC, George A, Martin C, Pierre CLS, Sanches T, Bimschleger HV, Gao J, Cheng R, Nguyen KM, Holl KL, Polesskaya O, Ishiwari K, Chen H, Woods LCS, Palmer AA, Robinson TE, Flagel SB, Meyer PJ. Genomic Loci Influencing Cue-Reactivity in Heterogeneous Stock Rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584852. [PMID: 38559127 PMCID: PMC10980002 DOI: 10.1101/2024.03.13.584852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Addiction vulnerability is associated with the tendency to attribute incentive salience to reward predictive cues; both addiction and the attribution of incentive salience are influenced by environmental and genetic factors. To characterize the genetic contributions to incentive salience attribution, we performed a genome-wide association study (GWAS) in a cohort of 1,645 genetically diverse heterogeneous stock (HS) rats. We tested HS rats in a Pavlovian conditioned approach task, in which we characterized the individual responses to food-associated stimuli ("cues"). Rats exhibited either cue-directed "sign-tracking" behavior or food-cup directed "goal-tracking" behavior. We then used the conditioned reinforcement procedure to determine whether rats would perform a novel operant response for unrewarded presentations of the cue. We found that these measures were moderately heritable (SNP heritability, h2 = .189-.215). GWAS identified 14 quantitative trait loci (QTLs) for 11 of the 12 traits we examined. Interval sizes of these QTLs varied widely. 7 traits shared a QTL on chromosome 1 that contained a few genes (e.g. Tenm4, Mir708) that have been associated with substance use disorders and other mental health traits in humans. Other candidate genes (e.g. Wnt11, Pak1) in this region had coding variants and expression-QTLs in mesocorticolimbic regions of the brain. We also conducted a Phenome-Wide Association Study (PheWAS) on other behavioral measures in HS rats and found that regions containing QTLs on chromosome 1 were also associated with nicotine self-administration in a separate cohort of HS rats. These results provide a starting point for the molecular genetic dissection of incentive salience and provide further support for a relationship between attribution of incentive salience and drug abuse-related traits.
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Affiliation(s)
- Christopher P. King
- Department of Psychology, University at Buffalo, Buffalo, USA
- Clinical and Research Institute on Addictions, Buffalo, USA
| | - Apurva S. Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | | | - Jordan A. Tripi
- Department of Psychology, University at Buffalo, Buffalo, USA
| | - Alesa R. Hughson
- Department of Psychology, University of Michigan, Ann Arbor, USA
| | - Aidan P. Horvath
- Department of Psychology, University of Michigan, Ann Arbor, USA
| | | | - Anthony George
- Clinical and Research Institute on Addictions, Buffalo, USA
| | - Connor Martin
- Clinical and Research Institute on Addictions, Buffalo, USA
| | | | - Thiago Sanches
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | | | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Katie L. Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Keita Ishiwari
- Clinical and Research Institute on Addictions, Buffalo, USA
- Department of Pharmacology and Toxicology, University at Buffalo, Buffalo USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, USA
| | - Leah C. Solberg Woods
- Department of Internal Medicine, Molecular Medicine, Center on Diabetes, Obesity and Metabolism, Wake Forest School of Medicine, Winston-Salem, USA
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, USA
| | | | - Shelly B. Flagel
- Department of Psychiatry, University of Michigan, Ann Arbor, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
| | - Paul J. Meyer
- Department of Psychology, University at Buffalo, Buffalo, USA
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9
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Ninoyu Y, Friedman RA. The genetic landscape of age-related hearing loss. Trends Genet 2024; 40:228-237. [PMID: 38161109 DOI: 10.1016/j.tig.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Age-related hearing loss (ARHL) is a prevalent concern in the elderly population. Recent genome-wide and phenome-wide association studies (GWASs and PheWASs) have delved into the identification of causative variants and the understanding of pleiotropy, highlighting the polygenic intricacies of this complex condition. While recent large-scale GWASs have pinpointed significant SNPs and risk variants associated with ARHL, the detailed mechanisms, encompassing both genetic and epigenetic modifications, remain to be fully elucidated. This review presents the latest advances in association studies, integrating findings from both human studies and model organisms. By juxtaposing historical perspectives with contemporary genomics, we aim to catalyze innovative research and foster the development of novel therapeutic strategies for ARHL.
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Affiliation(s)
- Yuzuru Ninoyu
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Rick A Friedman
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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Holloway AL, Lerner TN. Hidden variables in stress neurobiology research. Trends Neurosci 2024; 47:9-17. [PMID: 37985263 PMCID: PMC10842876 DOI: 10.1016/j.tins.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
Among the central goals of stress neurobiology research is to understand the mechanisms by which stressors change neural circuit function to precipitate or exacerbate psychiatric symptoms. Yet despite decades of effort, psychiatric medications that target the biological substrates of the stress response are largely lacking. We propose that the clinical advancement of stress response-based therapeutics for psychiatric disorders may be hindered by 'hidden variables' in stress research, including considerations of behavioral study design (stressors and outcome measures), individual variability, sex differences, and the interaction of the body's stress hormone system with endogenous circadian and ultradian rhythms. We highlight key issues and suggest ways forward in stress neurobiology research that may improve the ability to assess stress mechanisms and translate preclinical findings.
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Affiliation(s)
- Ashley L Holloway
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Northwestern University Interdepartmental Neuroscience Program (NUIN), Evanston, IL, USA
| | - Talia N Lerner
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Northwestern University Interdepartmental Neuroscience Program (NUIN), Evanston, IL, USA.
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11
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Borrelli KN, Wingfield KK, Yao EJ, Zamorano CA, Sena KD, Beierle JA, Roos MA, Zhang H, Wachman EM, Bryant CD. Decreased myelin-related gene expression in the nucleus accumbens during spontaneous neonatal opioid withdrawal in the absence of long-term behavioral effects in adult outbred CFW mice. Neuropharmacology 2023; 240:109732. [PMID: 37774943 PMCID: PMC10598517 DOI: 10.1016/j.neuropharm.2023.109732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023]
Abstract
Prenatal opioid exposure is a major health concern in the United States, with the incidence of neonatal opioid withdrawal syndrome (NOWS) escalating in recent years. NOWS occurs upon cessation of in utero opioid exposure and is characterized by increased irritability, disrupted sleep patterns, high-pitched crying, and dysregulated feeding. The main pharmacological strategy for alleviating symptoms is treatment with replacement opioids. The neural mechanisms mediating NOWS and the long-term neurobehavioral effects are poorly understood. We used a third trimester-approximate model in which neonatal outbred pups (Carworth Farms White; CFW) were administered once-daily morphine (15 mg/kg, s.c.) from postnatal day (P) day 1 through P14 and were then assessed for behavioral and transcriptomic adaptations within the nucleus accumbens (NAc) on P15. We also investigated the long-term effects of perinatal morphine exposure on adult learning and reward sensitivity. We observed significant weight deficits, spontaneous thermal hyperalgesia, and altered ultrasonic vocalization (USV) profiles following repeated morphine and during spontaneous withdrawal. Transcriptome analysis of NAc from opioid-withdrawn P15 neonates via bulk mRNA sequencing identified an enrichment profile consistent with downregulation of myelin-associated transcripts. Despite the neonatal behavioral and molecular effects, there were no significant long-term effects of perinatal morphine exposure on adult spatial memory function in the Barnes Maze, emotional learning in fear conditioning, or in baseline or methamphetamine-potentiated reward sensitivity as measured via intracranial self-stimulation. Thus, the once daily third trimester-approximate exposure regimen, while inducing NOWS model traits and significant transcriptomic effects in neonates, had no significant long-term effects on adult behaviors.
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Affiliation(s)
- Kristyn N Borrelli
- Graduate Program for Neuroscience, Boston University, 610 Commonwealth Av, Boston, MA, 02215, USA; T32 Biomolecular Pharmacology PhD Program, Boston University Chobanian & Avedisian School of Medicine, USA; Boston University's Transformative Training Program in Addiction Science, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-317, Boston, MA, 02118, USA
| | - Kelly K Wingfield
- T32 Biomolecular Pharmacology PhD Program, Boston University Chobanian & Avedisian School of Medicine, USA; Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-606, Boston, MA, 02118, USA; Department of Pharmaceutical Sciences, Center for Drug Discovery, Northeastern University, 360 Huntington Av, 140 The Fenway Building, X138, Boston, MA, 02115, USA
| | - Emily J Yao
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-606, Boston, MA, 02118, USA; Department of Pharmaceutical Sciences, Center for Drug Discovery, Northeastern University, 360 Huntington Av, 140 The Fenway Building, X138, Boston, MA, 02115, USA
| | - Catalina A Zamorano
- Boston University's Undergraduate Research Opportunity Program, George Sherman Union, 775 Commonwealth Av, 5th floor, Boston, MA, 02215, USA
| | - Katherine D Sena
- Boston University's Undergraduate Research Opportunity Program, George Sherman Union, 775 Commonwealth Av, 5th floor, Boston, MA, 02215, USA
| | - Jacob A Beierle
- T32 Biomolecular Pharmacology PhD Program, Boston University Chobanian & Avedisian School of Medicine, USA; Boston University's Transformative Training Program in Addiction Science, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-317, Boston, MA, 02118, USA; Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-606, Boston, MA, 02118, USA; Department of Pharmaceutical Sciences, Center for Drug Discovery, Northeastern University, 360 Huntington Av, 140 The Fenway Building, X138, Boston, MA, 02115, USA
| | - Michelle A Roos
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-606, Boston, MA, 02118, USA; Department of Pharmaceutical Sciences, Center for Drug Discovery, Northeastern University, 360 Huntington Av, 140 The Fenway Building, X138, Boston, MA, 02115, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA
| | - Elisha M Wachman
- Department of Pediatrics, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, 1 Boston Medical Center Pl, Boston, MA, 02118, USA
| | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-606, Boston, MA, 02118, USA; Department of Pharmaceutical Sciences, Center for Drug Discovery, Northeastern University, 360 Huntington Av, 140 The Fenway Building, X138, Boston, MA, 02115, USA.
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12
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Brasher MS, Mize TJ, Thomas AL, Hoeffer CA, Ehringer MA, Evans LM. Testing associations between human anxiety and genes previously implicated by mouse anxiety models. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12851. [PMID: 37259642 PMCID: PMC10733569 DOI: 10.1111/gbb.12851] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
Anxiety disorders are common and can be debilitating, with effective treatments remaining hampered by an incomplete understanding of the underlying genetic etiology. Improvements have been made in understanding the genetic influences on mouse behavioral models of anxiety, yet it is unclear the extent to which genes identified in these experimental systems contribute to genetic variation in human anxiety phenotypes. Leveraging new and existing large-scale human genome-wide association studies, we tested whether sets of genes previously identified in mouse anxiety-like behavior studies contribute to a range of human anxiety disorders. When tested as individual genes, 13 mouse-identified genes were associated with human anxiety phenotypes, suggesting an overlap of individual genes contributing to both mouse models of anxiety-like behaviors and human anxiety traits. When genes were tested as sets, we did identify 14 significant associations between mouse gene sets and human anxiety, but the majority of gene sets showed no significant association with human anxiety phenotypes. These few significant associations indicate a need to identify and develop more translatable mouse models by identifying sets of genes that "match" between model systems and specific human phenotypes of interest. We suggest that continuing to develop improved behavioral paradigms and finer-scale experimental data, for instance from individual neuronal subtypes or cell-type-specific expression data, is likely to improve our understanding of the genetic etiology and underlying functional changes in anxiety disorders.
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Affiliation(s)
- Maizy S. Brasher
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
| | - Travis J. Mize
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
| | | | - Charles A. Hoeffer
- Institute for Behavioral GeneticsBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Marissa A. Ehringer
- Institute for Behavioral GeneticsBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Luke M. Evans
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
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13
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Boussaty EC, Tedeschi N, Novotny M, Ninoyu Y, Du E, Draf C, Zhang Y, Manor U, Scheuermann RH, Friedman R. Cochlear transcriptome analysis of an outbred mouse population (CFW). Front Cell Neurosci 2023; 17:1256619. [PMID: 38094513 PMCID: PMC10716316 DOI: 10.3389/fncel.2023.1256619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/11/2023] [Indexed: 12/20/2023] Open
Abstract
Age-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types, and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach-first by linking to expression of known marker genes, then using the NSForest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website, and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes within the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.
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Affiliation(s)
- Ely Cheikh Boussaty
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Neil Tedeschi
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Mark Novotny
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Yuzuru Ninoyu
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Eric Du
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Clara Draf
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Uri Manor
- Department of Cell and Developmental Biology, University of California San Diego, Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, CA, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Rick Friedman
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
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Xu J, Casanave R, Chitre AS, Wang Q, Nguyen KM, Blake C, Wagle M, Cheng R, Polesskaya O, Palmer AA, Guo S. Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556529. [PMID: 37732200 PMCID: PMC10508786 DOI: 10.1101/2023.09.06.556529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Behavioral diversity is critical for population fitness. Individual differences in risk-taking are observed across species, but underlying genetic mechanisms and conservation are largely unknown. We examined dark avoidance in larval zebrafish, a motivated behavior reflecting an approach-avoidance conflict. Brain-wide calcium imaging revealed significant neural activity differences between approach-inclined versus avoidance-inclined individuals. We used a population of ∼6,000 to perform the first genome-wide association study (GWAS) in zebrafish, which identified 34 genomic regions harboring many genes that are involved in synaptic transmission and human psychiatric diseases. We used CRISPR to study several causal genes: serotonin receptor-1b ( htr1b ), nitric oxide synthase-1 ( nos1 ), and stress-induced phosphoprotein-1 ( stip1 ). We further identified 52 conserved elements containing 66 GWAS significant variants. One encoded an exonic regulatory element that influenced tissue-specific nos1 expression. Together, these findings reveal new genetic loci and establish a powerful, scalable animal system to probe mechanisms underlying motivation, a critical dimension of psychiatric diseases.
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15
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Borrelli KN, Wingfield KK, Yao EJ, Zamorano CA, Sena KD, Beierle JA, Roos MA, Zhang H, Wachman EM, Bryant CD. Decreased myelin-related gene expression in the nucleus accumbens during spontaneous neonatal opioid withdrawal in the absence of long-term behavioral effects in adult outbred CFW mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552033. [PMID: 37609129 PMCID: PMC10441327 DOI: 10.1101/2023.08.04.552033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Prenatal opioid exposure is a major health concern in the United States, with the incidence of neonatal opioid withdrawal syndrome (NOWS) escalating in recent years. NOWS occurs upon cessation of in utero opioid exposure and is characterized by increased irritability, disrupted sleep patterns, high-pitched crying, and dysregulated feeding. The main pharmacological strategy for alleviating symptoms is treatment with replacement opioids. The neural mechanisms mediating NOWS and the long-term neurobehavioral effects are poorly understood. We used a third trimester-approximate model in which neonatal outbred pups (Carworth Farms White; CFW) were administered once-daily morphine (15 mg/kg, s.c.) from postnatal day (P) day 1 through P14 and were then assessed for behavioral and transcriptomic adaptations within the nucleus accumbens (NAc) on P15. We also investigated the long-term effects of perinatal morphine exposure on adult learning and reward sensitivity. We observed significant weight deficits, spontaneous thermal hyperalgesia, and altered ultrasonic vocalization (USV) profiles following repeated morphine and during spontaneous withdrawal. Transcriptome analysis of NAc from opioid-withdrawn P15 neonates via bulk mRNA sequencing identified an enrichment profile consistent with downregulation of myelin-associated transcripts. Despite the neonatal behavioral and molecular effects, there were no significant long-term effects of perinatal morphine exposure on adult spatial memory function in the Barnes Maze, emotional learning in fear conditioning, or in baseline or methamphetamine-potentiated reward sensitivity as measured via intracranial self-stimulation. Thus, the once daily third trimester-approximate exposure regimen, while inducing NOWS model traits and significant transcriptomic effects in neonates, had no significant long-term effects on adult behaviors. HIGHLIGHTS We replicated some NOWS model traits via 1x-daily morphine (P1-P14).We found a downregulation of myelination genes in nucleus accumbens on P15.There were no effects on learning/memory or reward sensitivity in adults.
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Affiliation(s)
- Kristyn N. Borrelli
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., L-606B, Boston, MA 02118
- Graduate Program for Neuroscience, Boston University, 610 Commonwealth Av, Boston, MA 02215
- Boston University’s Transformative Training Program in Addiction Science, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-317, Boston, MA 02118
| | - Kelly K. Wingfield
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., L-606B, Boston, MA 02118
- T32 Biomolecular Pharmacology PhD Program, Boston University Chobanian and Avedisian School of Medicine
| | - Emily J. Yao
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., L-606B, Boston, MA 02118
| | - Catalina A. Zamorano
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., L-606B, Boston, MA 02118
- Boston University’s Undergraduate Research Opportunity Program, George Sherman Union, 775 Commonwealth Av, 5 floor, Boston, MA 02215
| | - Katherine D. Sena
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., L-606B, Boston, MA 02118
- Boston University’s Undergraduate Research Opportunity Program, George Sherman Union, 775 Commonwealth Av, 5 floor, Boston, MA 02215
| | - Jacob A. Beierle
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., L-606B, Boston, MA 02118
- T32 Biomolecular Pharmacology PhD Program, Boston University Chobanian and Avedisian School of Medicine
- Boston University’s Transformative Training Program in Addiction Science, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., L-317, Boston, MA 02118
| | - Michelle A. Roos
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., L-606B, Boston, MA 02118
| | - Huiping Zhang
- Department of Psychiatry, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., Boston, MA 02118
| | - Elisha M. Wachman
- Department of Pediatrics, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, 1 Boston Medical Center Pl, Boston, MA 02118
| | - Camron D. Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., L-606B, Boston, MA 02118
- Department of Psychiatry, Boston University Chobanian and Avedisian School of Medicine, 72 E. Concord St., Boston, MA 02118
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Boussaty EC, Tedeschi N, Novotny M, Ninoyu Y, Du E, Draf C, Zhang Y, Manor U, Scheuermann RH, Friedman R. Cochlear transcriptome analysis of an outbred mouse population (CFW). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528661. [PMID: 36824745 PMCID: PMC9948975 DOI: 10.1101/2023.02.15.528661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Age-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach - first by linking to expression of known marker genes, then using the NS-Forest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website (https://umgear.org/), and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes withing the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.
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Affiliation(s)
| | | | | | - Yuzuru Ninoyu
- Department of Otolaryngology, University of California, San Diego, CA
| | - Eric Du
- Department of Otolaryngology, University of California, San Diego, CA
| | - Clara Draf
- Department of Otolaryngology, University of California, San Diego, CA
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA
| | - Uri Manor
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, CA, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA
- Department of Pathology, University of California, San Diego, CA
| | - Rick Friedman
- Department of Otolaryngology, University of California, San Diego, CA
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Bennett TM, Zhou Y, Meyer KJ, Anderson MG, Shiels A. Whole-exome sequencing prioritizes candidate genes for hereditary cataract in the Emory mouse mutant. G3 (BETHESDA, MD.) 2023; 13:jkad055. [PMID: 36891866 PMCID: PMC10151407 DOI: 10.1093/g3journal/jkad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/10/2023]
Abstract
The Emory cataract (Em) mouse mutant has long been proposed as an animal model for age-related or senile cataract in humans-a leading cause of visual impairment. However, the genetic defect(s) underlying the autosomal dominant Em phenotype remains elusive. Here, we confirmed development of the cataract phenotype in commercially available Em/J mice [but not ancestral Carworth Farms White (CFW) mice] at 6-8 months of age and undertook whole-exome sequencing of candidate genes for Em. Analysis of coding and splice-site variants did not identify any disease-causing/associated mutations in over 450 genes known to underlie inherited and age-related forms of cataract and other lens disorders in humans and mice, including genes for lens crystallins, membrane/cytoskeleton proteins, DNA/RNA-binding proteins, and those associated with syndromic/systemic forms of cataract. However, we identified three cataract/lens-associated genes each with one novel homozygous variant including predicted missense substitutions in Prx (p.R167C) and Adamts10 (p.P761L) and a disruptive in-frame deletion variant (predicted missense) in Abhd12 (p.L30_A32delinsS) that were absent in CFW and over 35 other mouse strains. In silico analysis predicted that the missense substitutions in Prx and Adamts10 were borderline neutral/damaging and neutral, respectively, at the protein function level, whereas, that in Abhd12 was functionally damaging. Both the human counterparts of Adamts10 and Abhd12 are clinically associated with syndromic forms of cataract known as Weil-Marchesani syndrome 1 and polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract syndrome, respectively. Overall, while we cannot exclude Prx and Adamts10, our data suggest that Abhd12 is a promising candidate gene for cataract in the Em/J mouse.
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Affiliation(s)
- Thomas M Bennett
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yuefang Zhou
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kacie J Meyer
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
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18
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Booher WC, Vanderlinden LA, Hall LA, Thomas AL, Evans LM, Saba LM, Ehringer MA. Hippocampal RNA sequencing in mice selectively bred for high and low activity. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12832. [PMID: 36514243 PMCID: PMC10067415 DOI: 10.1111/gbb.12832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022]
Abstract
High and Low Activity strains of mice were bidirectionally selected for differences in open-field activity (DeFries et al., 1978, Behavior Genetics, 8: 3-13) and subsequently inbred to use as a genetic model for studying anxiety-like behaviors (Booher et al., 2021, Genes, Brain and Behavior, 20: e12730). Hippocampal RNA-sequencing of the High and Low Activity mice identified 3901 differentially expressed protein-coding genes, with both sex-dependent and sex-independent effects. Functional enrichment analysis (PANTHER) highlighted 15 gene ontology terms, which allowed us to create a narrow list of 264 top candidate genes. Of the top candidate genes, 46 encoded four Complexes (I, II, IV and V) and two electron carriers (cytochrome c and ubiquinone) of the mitochondrial oxidative phosphorylation process. The most striking results were in the female high anxiety, Low Activity mice, where 39/46 genes relating to oxidative phosphorylation were upregulated. In addition, comparison of our top candidate genes with two previously curated High and Low Activity gene lists highlight 24 overlapping genes, where Ndufa13, which encodes the supernumerary subunit A13 of complex I, was the only gene to be included in all three lists. Mitochondrial dysfunction has recently been implicated as both a cause and effect of anxiety-related disorders and thus should be further explored as a possible novel pharmaceutical treatment for anxiety disorders.
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Affiliation(s)
- Winona C. Booher
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Institute for Behavioral GeneticsUniversity of Colorado BoulderBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Lauren A. Vanderlinden
- Department of Biostatistics & Informatics, Colorado School of Public HealthUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Lucy A. Hall
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Aimee L. Thomas
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Luke M. Evans
- Institute for Behavioral GeneticsUniversity of Colorado BoulderBoulderColoradoUSA
| | - Laura M. Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Marissa A. Ehringer
- Institute for Behavioral GeneticsUniversity of Colorado BoulderBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
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19
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Munro D, Wang T, Chitre AS, Polesskaya O, Ehsan N, Gao J, Gusev A, Woods LS, Saba L, Chen H, Palmer A, Mohammadi P. The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats. Nucleic Acids Res 2022; 50:10882-10895. [PMID: 36263809 PMCID: PMC9638908 DOI: 10.1093/nar/gkac912] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/17/2022] [Accepted: 10/05/2022] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous Stock (HS) rats are a genetically diverse outbred rat population that is widely used for studying genetics of behavioral and physiological traits. Mapping Quantitative Trait Loci (QTL) associated with transcriptional changes would help to identify mechanisms underlying these traits. We generated genotype and transcriptome data for five brain regions from 88 HS rats. We identified 21 392 cis-QTLs associated with expression and splicing changes across all five brain regions and validated their effects using allele specific expression data. We identified 80 cases where eQTLs were colocalized with genome-wide association study (GWAS) results from nine physiological traits. Comparing our dataset to human data from the Genotype-Tissue Expression (GTEx) project, we found that the HS rat data yields twice as many significant eQTLs as a similarly sized human dataset. We also identified a modest but highly significant correlation between genetic regulatory variation among orthologous genes. Surprisingly, we found less genetic variation in gene regulation in HS rats relative to humans, though we still found eQTLs for the orthologs of many human genes for which eQTLs had not been found. These data are available from the RatGTEx data portal (RatGTEx.org) and will enable new discoveries of the genetic influences of complex traits.
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Affiliation(s)
- Daniel Munro
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Nava Ehsan
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Leah C Solberg Woods
- Section of Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Abraham A Palmer
- Correspondence may also be addressed to Abraham A. Palmer. Tel: +1 858 534 2093;
| | - Pejman Mohammadi
- To whom correspondence should be addressed. Tel: +1 858 784 8746;
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20
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Du EY, Boussaty EC, La Monte OA, Dixon PR, Zhou TY, Friedman RA. Large-scale phenotyping and characterization of age-related hearing loss in outbred CFW mice. Hear Res 2022; 424:108605. [PMID: 36088865 DOI: 10.1016/j.heares.2022.108605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/27/2022] [Accepted: 09/03/2022] [Indexed: 11/18/2022]
Abstract
Age-related hearing loss (ARHL), or presbycusis, is one of the most prevalent conditions affecting the global population. A substantial fraction of patients with ARHL have no identifiable mutation despite over a hundred having been discovered, suggesting unidentified monogenic or polygenic causes. In this study, we investigated the hearing function of the aging outbred CFW mice through auditory brainstem response (ABR) thresholds. Through the characterization of 1,132 ABRs, we observed significant variation in both absolute thresholds and the effect of aging. We identify eight distinct patterns of hearing loss and were able to categorize nearly all data within these eight categories. Proportions within each category varied immensely between aging timepoints. We observe a small but consistent hearing deficit in female CFW mice. The resulting phenotypic data are a necessity for ARHL association mapping at a higher resolution than has previously been achieved and provides a new resource for studying ARHL.
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Affiliation(s)
- Eric Y Du
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Ely C Boussaty
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Olivia A La Monte
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA; University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Peter R Dixon
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Thomas Y Zhou
- University of California, San Diego, La Jolla, CA, USA
| | - Rick A Friedman
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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21
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Wright KM, Deighan AG, Di Francesco A, Freund A, Jojic V, Churchill GA, Raj A. Age and diet shape the genetic architecture of body weight in diversity outbred mice. eLife 2022; 11:64329. [PMID: 35838135 PMCID: PMC9286741 DOI: 10.7554/elife.64329] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/20/2022] [Indexed: 12/26/2022] Open
Abstract
Understanding how genetic variation shapes a complex trait relies on accurately quantifying both the additive genetic and genotype–environment interaction effects in an age-dependent manner. We used a linear mixed model to quantify diet-dependent genetic contributions to body weight measured through adulthood in diversity outbred female mice under five diets. We observed that heritability of body weight declined with age under all diets, except the 40% calorie restriction diet. We identified 14 loci with age-dependent associations and 19 loci with age- and diet-dependent associations, with many diet-dependent loci previously linked to neurological function and behavior in mice or humans. We found their allelic effects to be dynamic with respect to genomic background, age, and diet, identifying several loci where distinct alleles affect body weight at different ages. These results enable us to more fully understand and predict the effectiveness of dietary intervention on overall health throughout age in distinct genetic backgrounds. Body weight is one trait influenced by genes, age and environmental factors. Both internal and external environmental pressures are known to affect genetic variation over time. However, it is largely unknown how all factors – including age – interact to shape metabolism and bodyweight. Wright et al. set out to quantify the interactions between genes and diet in ageing mice and found that the effect of genetics on mouse body weight changes with age. In the experiments, Wright et al. weighed 960 female mice with diverse genetic backgrounds, starting at two months of age into adulthood. The animals were randomized to different diets at six months of age. Some mice had unlimited food access, others received 20% or 40% less calories than a typical mouse diet, and some fasted one or two days per week. Variations in their genetic background explained about 80% of differences in mice’s weight, but the influence of genetics relative to non-genetic factors decreased as they aged. Mice on the 40% calorie restriction diet were an exception to this rule and genetics accounted for 80% of their weight throughout adulthood, likely due to reduced influence from diet and reduced interactions between diet and genes. Several genes involved in metabolism, neurological function, or behavior, were associated with mouse weight. The experiments highlight the importance of considering interactions between genetics, environment, and age in determining complex traits like body weight. The results and the approaches used by Wright et al. may help other scientists learn more about how the genetic predisposition to disease changes with environmental stimuli and age.
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Affiliation(s)
- Kevin M Wright
- Calico Life Sciences LLC, South San Francisco, United States
| | | | | | - Adam Freund
- Calico Life Sciences LLC, South San Francisco, United States
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, United States
| | | | - Anil Raj
- Calico Life Sciences LLC, South San Francisco, United States
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22
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Buhusi CV, Meyer AE, Oprisan SA, Buhusi M. Not All Mice Are Created Equal: Interval Timing Accuracy and Scalar Timing in 129, Swiss-Webster, and C57BL/6 Mice. TIMING & TIME PERCEPTION 2022; 11:242-262. [PMID: 37065684 PMCID: PMC10103834 DOI: 10.1163/22134468-bja10052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Many species, including humans, show both accurate timing − appropriate time estimation in the seconds to minutes range − and scalar timing − time estimation error varies linearly with estimated duration. Behavioral paradigms aimed at investigating interval timing are expected to evaluate these dissociable characteristics of timing. However, when evaluating interval timing in models of neuropsychiatric disease, researchers are confronted with a lack of adequate studies about the parent (background) strains, since accuracy and scalar timing have only been demonstrated for the C57BL/6 strain of mice (Buhusi, Aziz, Winslow, Carter, Swearingen, & Buhusi (2009) Behav. Neurosci., 123, 1102–1113). We used a peak-interval (PI) procedure with three intervals − a protocol in which other species, including humans, demonstrate accurate, scalar timing − to evaluate timing accuracy and scalar timing in three strains of mice frequently used in genetic and behavioral studies: 129, Swiss-Webster (SW), and C57BL/6. C57BL/6 mice showed accurate, scalar timing, while 129 and SW mice showed departures from accuracy and/or scalar timing. Results suggest that the genetic background/strain of the mouse is a critical variable for studies investigating interval timing in genetically engineered mice. Our study validates the PI procedure with multiple intervals as a proper technique, and the C57BL/6 strain as the most suitable genetic background to date for behavioral investigations of interval timing in genetically engineered mice modeling human disorders. In contrast, studies using mice in 129, SW, or mixed-background strains should be interpreted with caution, and thorough investigations of accuracy and scalar timing should be conducted before a less studied strain of mouse is considered for use in timing studies.
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Affiliation(s)
- Catalin V. Buhusi
- Neuroscience Program, Department of Psychology, Utah State University, Logan, UT 84322, USA
| | - Abby E. Meyer
- Department of Physics and Astronomy, College of Charleston, Charleston, SC 29424, USA
| | - Sorinel A. Oprisan
- Department of Physics and Astronomy, College of Charleston, Charleston, SC 29424, USA
| | - Mona Buhusi
- Neuroscience Program, Department of Psychology, Utah State University, Logan, UT 84322, USA
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23
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Widmayer SJ, Evans KS, Zdraljevic S, Andersen EC. Evaluating the power and limitations of genome-wide association studies in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2022; 12:jkac114. [PMID: 35536194 PMCID: PMC9258552 DOI: 10.1093/g3journal/jkac114] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022]
Abstract
Quantitative genetics in Caenorhabditis elegans seeks to identify naturally segregating genetic variants that underlie complex traits. Genome-wide association studies scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci. Genome-wide association studies are a popular choice for quantitative genetic analyses because the quantitative trait loci that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of genome-wide association study has not, to date, been formally evaluated in C. elegans. We developed an open-source genome-wide association study pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance in collections of wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of quantitative trait loci detected by genome-wide association studies. Power to detect smaller-effect quantitative trait loci increased with the number of strains sampled from the C. elegans Natural Diversity Resource. Population structure was a major driver of variation in mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous genome-wide association studies of experimentally validated quantitative trait variants. Our simulation-based evaluation of performance provides the community with critical context to pursue quantitative genetic studies using the C. elegans Natural Diversity Resource to elucidate the genetic basis of complex traits in C. elegans natural populations.
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Affiliation(s)
- Samuel J Widmayer
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Kathryn S Evans
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Stefan Zdraljevic
- Department of Biological Chemistry, University of California—Los Angeles, Los Angeles, CA 90095, USA
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
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24
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Li W, Liu J, Zhang H, Liu Z, Wang Y, Xing L, He Q, Du H. Plant pan-genomics: recent advances, new challenges, and roads ahead. J Genet Genomics 2022; 49:833-846. [PMID: 35750315 DOI: 10.1016/j.jgg.2022.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 10/18/2022]
Abstract
Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species, and for providing information for plant improvement. Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs. Nevertheless, pan-genomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers of samples, ineffective integration of big data, and difficulty in applying it to downstream multi-omics analysis and breeding research. In this review, we summarize the definition and recent achievements of plant pan-genomics, computational technologies used for pan-genome construction, and the applications of pan-genomes in plant genomics and molecular breeding. We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection, genome assembly and annotation, structural variation identification, and construction and application of graph-based pan-genomes. The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution, crop domestication, and phenotypic diversity for future studies.
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Affiliation(s)
- Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Jianan Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Yu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Longsheng Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China.
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25
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Yang L, Zhang Y, Song Y, Zhang H, Yang R. Canonical transformation for multivariate mixed model association analyses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2147-2155. [PMID: 35536304 DOI: 10.1007/s00122-022-04103-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
In extension of Single-RunKing to analyze multiple correlated traits, mvRunKing not only enlarged number of the analyzed phenotypes with canonical transformation, but also improved statistical power to detect pleiotropic QTNs through joint association analysis. Based on genomic variance-covariance matrices, we simplified multivariate mixed model association analysis to multiple univariate ones by using canonical transformation, and then individually implemented univariate association tests in the Single-RunKing. which enlarged number of the analyzed phenotypes. With canonical transformation back to the original scale, the association results would be biologically interpretable. Especially, we rapidly estimated genomic variance-covariance matrices with multivariate GEMMA and optimized separately the polygenic variances (or heritabilities) for only the markers that had large effects or higher significance levels in univariate mixed models, greatly improving computing efficiency for multiple univariate association tests. Beyond one test at once, joint association analysis for quantitative trait nucleotide (QTN) candidates can significantly increase statistical powers to detect QTNs. A user-friendly mvRunKing software was developed to efficiently implement multivariate mixed model association analyses.
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Affiliation(s)
- Li'ang Yang
- College of Life Science and College of Animal Scientific and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yuxin Song
- Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Hengyu Zhang
- Department of Information and Computing Science, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Runqing Yang
- Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
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26
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Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies. PLoS Genet 2022; 18:e1010234. [PMID: 35639796 PMCID: PMC9187121 DOI: 10.1371/journal.pgen.1010234] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 06/10/2022] [Accepted: 05/03/2022] [Indexed: 12/30/2022] Open
Abstract
Sprague Dawley (SD) rats are among the most widely used outbred laboratory rat populations. Despite this, the genetic characteristics of SD rats have not been clearly described, and SD rats are rarely used for experiments aimed at exploring genotype-phenotype relationships. In order to use SD rats to perform a genome-wide association study (GWAS), we collected behavioral data from 4,625 SD rats that were predominantly obtained from two commercial vendors, Charles River Laboratories and Harlan Sprague Dawley Inc. Using double-digest genotyping-by-sequencing (ddGBS), we obtained dense, high-quality genotypes at 291,438 SNPs across 4,061 rats. This genetic data allowed us to characterize the variation present in Charles River vs. Harlan SD rats. We found that the two populations are highly diverged (FST > 0.4). Furthermore, even for rats obtained from the same vendor, there was strong population structure across breeding facilities and even between rooms at the same facility. We performed multiple separate GWAS by fitting a linear mixed model that accounted for population structure and using meta-analysis to jointly analyze all cohorts. Our study examined Pavlovian conditioned approach (PavCA) behavior, which assesses the propensity for rats to attribute incentive salience to reward-associated cues. We identified 46 significant associations for the various metrics used to define PavCA. The surprising degree of population structure among SD rats from different sources has important implications for their use in both genetic and non-genetic studies. Outbred Sprague Dawley rats are among the most commonly used rats for neuroscience, physiology and pharmacological research; in the year 2020, 4,188 publications contained the keyword “Sprague Dawley”. Rats identified as “Sprague Dawley” are sold by several commercial vendors, including Charles River Laboratories and Harlan Sprague Dawley Inc. (now Envigo). Despite their widespread use, little is known about the genetic diversity of SD. We genotyped more than 4,000 SD rats, which we used for a genome-wide association study (GWAS) and to characterize genetic differences between SD rats from Charles River Laboratories and Harlan. Our analysis revealed extensive population structure both between and within vendors. The GWAS for Pavlovian conditioned approach (PavCA) identified a number of genome-wide significant loci for that complex behavioral trait. Our results demonstrate that, despite sharing an identical name, SD rats that are obtained from different vendors are very different. Future studies should carefully define the exact source of SD rats being used and may exploit their genetic diversity for genetic studies of complex traits.
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27
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Zhang Q, Yi GY. Generalized network structured models with mixed responses subject to measurement error and misclassification. Biometrics 2022. [PMID: 35032335 DOI: 10.1111/biom.13623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
Research of complex associations between a gene network and multiple responses has attracted extensive attention. A great challenge in analyzing genetic data is posited by the presence of the genetic network that is typically unknown in applications. Moreover, mismeasurement of responses introduces additional complexity to distort usual inferential procedures. In this paper, we consider the problem with mixed binary and continuous responses which are subject to mismeasurement and associated with complex structured covariates. We first start with the case where data are precisely measured. We propose a generalized network structured model and develop a two-step inferential procedure. In the first step, we employ a Gaussian graphical model to facilitate the covariates network structure, and in the second step, we incorporate the estimated graphical structure of covariates and develop an estimating equation method. Furthermore, we extend the development to accommodating mismeasured responses. We consider two cases where the information on mismeasurement is either known or estimated from a validation sample. Theoretical results are established and numerical studies are conducted to evaluate the finite sample performance of the proposed methods. We apply the proposed method to analyze the outbred Carworth Farms White mice data arising from a genome-wide association study. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qihuang Zhang
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Grace Y Yi
- Department of Statistical and Actuarial Sciences, Department of Computer Science, University of Western Ontario, London, N6A 5B7, Canada
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28
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Zou J, Gopalakrishnan S, Parker CC, Nicod J, Mott R, Cai N, Lionikas A, Davies RW, Palmer AA, Flint J. Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility. G3 (BETHESDA, MD.) 2022; 12:jkab394. [PMID: 34791208 PMCID: PMC8728023 DOI: 10.1093/g3journal/jkab394] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/17/2021] [Indexed: 12/12/2022]
Abstract
Combining samples for genetic association is standard practice in human genetic analysis of complex traits, but is rarely undertaken in rodent genetics. Here, using 23 phenotypes and genotypes from two independent laboratories, we obtained a sample size of 3076 commercially available outbred mice and identified 70 loci, more than double the number of loci identified in the component studies. Fine-mapping in the combined sample reduced the number of likely causal variants, with a median reduction in set size of 51%, and indicated novel gene associations, including Pnpo, Ttll6, and GM11545 with bone mineral density, and Psmb9 with weight. However, replication at a nominal threshold of 0.05 between the two component studies was low, with less than one-third of loci identified in one study replicated in the second. In addition to overestimates in the effect size in the discovery sample (Winner's Curse), we also found that heterogeneity between studies explained the poor replication, but the contribution of these two factors varied among traits. Leveraging these observations, we integrated information about replication rates, study-specific heterogeneity, and Winner's Curse corrected estimates of power to assign variants to one of four confidence levels. Our approach addresses concerns about reproducibility and demonstrates how to obtain robust results from mapping complex traits in any genome-wide association study.
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Affiliation(s)
- Jennifer Zou
- Department of Computer Science, University of California, Los Angeles, CA 90024, USA
| | - Shyam Gopalakrishnan
- Faculty of Health and Medical Sciences, GLOBE Institute, University of Copenhagen, Copenhagen DK-1353, Denmark
| | - Clarissa C Parker
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, VT 05753, USA
| | | | - Richard Mott
- UCL Department of Genetics, Evolution & Environment, UCL Genetics Institute, London WC1E 6BT, UK
| | - Na Cai
- Helmholtz Zentrum Muenchen, Helmoltz Pioneer Campus, Neuherberg 85764, Germany
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, College of Life Sciences and Medicine, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Robert W Davies
- Department of Statistics, University of Oxford, Oxford OX1 2JD, UK
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jonathan Flint
- Department of Biobehavioral Sciences, University of California, Los Angeles, CA 90024, USA
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29
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Zhang G, Deighan A, Raj A, Robinson L, Donato HJ, Garland G, Leland M, Martin-McNulty B, Kolumam GA, Riegler J, Freund A, Wright KM, Churchill GA. Intermittent fasting and caloric restriction interact with genetics to shape physiological health in mice. Genetics 2022; 220:iyab157. [PMID: 34791228 PMCID: PMC8733459 DOI: 10.1093/genetics/iyab157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/10/2021] [Indexed: 11/20/2022] Open
Abstract
Dietary interventions can dramatically affect physiological health and organismal lifespan. The degree to which organismal health is improved depends upon genotype and the severity of dietary intervention, but neither the effects of these factors, nor their interaction, have been quantified in an outbred population. Moreover, it is not well understood what physiological changes occur shortly after dietary change and how these may affect the health of an adult population. In this article, we investigated the effect of 6-month exposure of either caloric restriction (CR) or intermittent fasting (IF) on a broad range of physiological traits in 960 1-year old Diversity Outbred mice. We found CR and IF affected distinct aspects of physiology and neither the magnitude nor the direction (beneficial or detrimental) of effects were concordant with the severity of the intervention. In addition to the effects of diet, genetic variation significantly affected 31 of 36 traits (heritabilities ranged from 0.04 to 0.65). We observed significant covariation between many traits that was due to both diet and genetics and quantified these effects with phenotypic and genetic correlations. We genetically mapped 16 diet-independent and 2 diet-dependent significant quantitative trait loci, both of which were associated with cardiac physiology. Collectively, these results demonstrate the degree to which diet and genetics interact to shape the physiological health of adult mice following 6 months of dietary intervention.
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Affiliation(s)
- Guozhu Zhang
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | - Anil Raj
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | | | | | | | | | | | | | - Adam Freund
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Kevin M Wright
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
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30
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Goldberg LR, Yao EJ, Kelliher JC, Reed ER, Cox JW, Parks C, Kirkpatrick SL, Beierle JA, Chen MM, Johnson WE, Homanics GE, Williams RW, Bryant CD, Mulligan MK. A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity. GENES, BRAIN, AND BEHAVIOR 2021; 20:e12774. [PMID: 34677900 PMCID: PMC9083095 DOI: 10.1111/gbb.12774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/19/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022]
Abstract
Psychostimulant (methamphetamine, cocaine) use disorders have a genetic component that remains mostly unknown. We conducted genome-wide quantitative trait locus (QTL) analysis of methamphetamine stimulant sensitivity. To facilitate gene identification, we employed a Reduced Complexity Cross between closely related C57BL/6 mouse substrains and examined maximum speed and distance traveled over 30 min following methamphetamine (2 mg/kg, i.p.). For maximum methamphetamine-induced speed following the second and third administration, we identified a single genome-wide significant QTL on chromosome 11 that peaked near the Cyfip2 locus (LOD = 3.5, 4.2; peak = 21 cM [36 Mb]). For methamphetamine-induced distance traveled following the first and second administration, we identified a genome-wide significant QTL on chromosome 5 that peaked near a functional intronic indel in Gabra2 coding for the alpha-2 subunit of the GABA-A receptor (LOD = 3.6-5.2; peak = 34-35 cM [66-67 Mb]). Striatal cis-expression QTL mapping corroborated Gabra2 as a functional candidate gene underlying methamphetamine-induced distance traveled. CRISPR/Cas9-mediated correction of the mutant intronic deletion on the C57BL/6J background to the wild-type C57BL/6NJ allele was sufficient to reduce methamphetamine-induced locomotor activity toward the wild-type C57BL/6NJ-like level, thus validating the quantitative trait variant (QTV). These studies show the power and efficiency of Reduced Complexity Crosses in identifying causal variants underlying complex traits. Functionally restoring Gabra2 expression decreased methamphetamine stimulant sensitivity and supports preclinical and human genetic studies implicating the GABA-A receptor in psychostimulant addiction-relevant traits. Importantly, our findings have major implications for studying psychostimulants in the C57BL/6J strain-the gold standard strain in biomedical research.
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Affiliation(s)
- Lisa R. Goldberg
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
- NIGMS T32 Ph.D. Training Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Emily J. Yao
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - Julia C. Kelliher
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - Eric R. Reed
- Ph.D. Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
| | - Jiayi Wu Cox
- Program in Biomedical Sciences, Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Cory Parks
- Department of Agricultural, Biology, and Health Sciences, Cameron University, Lawton, Oklahoma, USA
| | - Stacey L. Kirkpatrick
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - Jacob A. Beierle
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
- NIGMS T32 Ph.D. Training Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Melanie M. Chen
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - William E. Johnson
- Department of Medicine, Computational Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Gregg E. Homanics
- Departments of Anesthesiology, Neurobiology, and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Camron D. Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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Oates S, Absoud M, Goyal S, Bayley S, Baulcomb J, Sims A, Riddett A, Allis K, Brasch-Andersen C, Balasubramanian M, Bai R, Callewaert B, Hüffmeier U, Le Duc D, Radtke M, Korff C, Kennedy J, Low K, Møller RS, Nielsen JEK, Popp B, Quteineh L, Rønde G, Schönewolf-Greulich B, Shillington A, Taylor MR, Todd E, Torring PM, Tümer Z, Vasileiou G, Yates TM, Zweier C, Rosch R, Basson MA, Pal DK. ZMYND11 variants are a novel cause of centrotemporal and generalised epilepsies with neurodevelopmental disorder. Clin Genet 2021; 100:412-429. [PMID: 34216016 DOI: 10.1111/cge.14023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022]
Abstract
ZMYND11 is the critical gene in chromosome 10p15.3 microdeletion syndrome, a syndromic cause of intellectual disability. The phenotype of ZMYND11 variants has recently been extended to autism and seizures. We expand on the epilepsy phenotype of 20 individuals with pathogenic variants in ZMYND11. We obtained clinical descriptions of 16 new and nine published individuals, plus detailed case history of two children. New individuals were identified through GeneMatcher, ClinVar and the European Network for Therapies in Rare Epilepsy (NETRE). Genetic evaluation was performed using gene panels or exome sequencing; variants were classified using American College of Medical Genetics (ACMG) criteria. Individuals with ZMYND11 associated epilepsy fell into three groups: (i) atypical benign partial epilepsy or idiopathic focal epilepsy (n = 8); (ii) generalised epilepsies/infantile epileptic encephalopathy (n = 4); (iii) unclassified (n = 8). Seizure prognosis ranged from spontaneous remission to drug resistant. Neurodevelopmental deficits were invariable. Dysmorphic features were variable. Variants were distributed across the gene and mostly de novo with no precise genotype-phenotype correlation. ZMYND11 is one of a small group of chromatin reader genes associated in the pathogenesis of epilepsy, and specifically ABPE. More detailed epilepsy descriptions of larger cohorts and functional studies might reveal genotype-phenotype correlation. The epileptogenic mechanism may be linked to interaction with histone H3.3.
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Affiliation(s)
- Stephanie Oates
- Department of Paediatric Neuroscience, King's College Hospital, London, UK
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, UK
| | - Michael Absoud
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
- Department of Women and Children's Health, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Sushma Goyal
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
| | - Sophie Bayley
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, UK
| | - Jennifer Baulcomb
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
| | - Annemarie Sims
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
| | - Amy Riddett
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
| | - Katrina Allis
- Genetic Counselor, Mitochondrial and Metabolic Genetics, GeneDx, Gaithersburg, Maryland, USA
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| | - Renkui Bai
- Genetic Counselor, Mitochondrial and Metabolic Genetics, GeneDx, Gaithersburg, Maryland, USA
| | - Bert Callewaert
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander Universitat of Erlangen-Nurnberg, Erlangen, Germany
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Medical Centre, Leipzig, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Centre, Leipzig, Germany
| | - Christian Korff
- Pediatric Neurology Unit, University Hospitals, Geneva, Switzerland
| | - Joanna Kennedy
- Department of Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Karen Low
- Department of Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Jens Erik Klint Nielsen
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Bernt Popp
- Institute of Human Genetics, Friedrich-Alexander Universitat of Erlangen-Nurnberg, Erlangen, Germany
| | - Lina Quteineh
- Pediatric Neurology Unit, University Hospitals, Geneva, Switzerland
- Service of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Gitte Rønde
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | | | | | - Matthew Rg Taylor
- University of Colorado Anschutz Medical Campus, Adult Medical Genetics Program, Aurora, Colorado, USA
| | - Emily Todd
- University of Colorado Anschutz Medical Campus, Adult Medical Genetics Program, Aurora, Colorado, USA
| | - Pernille M Torring
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Zeynep Tümer
- Department of Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander Universitat of Erlangen-Nurnberg, Erlangen, Germany
| | - T Michael Yates
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| | - Christiane Zweier
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Richard Rosch
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - M Albert Basson
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Deb K Pal
- Department of Paediatric Neuroscience, King's College Hospital, London, UK
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, UK
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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Booher WC, Hall LA, Thomas AL, Merhroff EA, Reyes Martínez GJ, Scanlon KE, Lowry CA, Ehringer MA. Anxiety-related defensive behavioral responses in mice selectively bred for High and Low Activity. GENES, BRAIN, AND BEHAVIOR 2021; 20:e12730. [PMID: 33786989 PMCID: PMC10846611 DOI: 10.1111/gbb.12730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/15/2022]
Abstract
High and Low Activity strains of mice (displaying low and high anxiety-like behavior, respectively) with 7.8-20 fold differences in open-field activity were selected and subsequently inbred to use as a genetic model for studying anxiety-like behavior in mice (DeFries et al., 1978, Behavior Genetics, 8:3-13). These strains exhibited differences in other anxiety-related behaviors as assessed using the light-dark box, elevated plus-maze, mirror chamber, and elevated square-maze tests (Henderson et al., 2004, Behavior Genetics, 34: 267-293). The purpose of these experiments was three-fold. First, we repeated a 6-day behavioral battery using updated equipment and software to confirm the extreme differences in anxiety-like behaviors. Second, we tested novel object exploration, a measure of anxiety-like behavior that does not rely heavily on locomotion. Third, we conducted a home cage wheel running experiment to determine whether these strains differ in locomotor activity in a familiar, home cage environment. Our behavioral test battery confirmed extreme differences in multiple measures of anxiety-like behaviors. Furthermore, the novel object test demonstrated that the High Activity mice exhibited decreased anxiety-like behaviors (increased nose pokes) compared to Low Activity mice. Finally, male Low Activity mice ran nearly twice as far each day on running wheels compared to High Activity mice, while female High and Low Activity mice did not differ in wheel running. These results support the idea that the behavioral differences between High and Low Activity mice are likely to be due to anxiety-related factors and not simply generalized differences in locomotor activity.
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Affiliation(s)
- Winona C. Booher
- Department of Integrative Physiology, University of
Colorado, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado,
Boulder, CO, USA
| | - Lucy A. Hall
- Department of Integrative Physiology, University of
Colorado, Boulder, CO, USA
| | - Aimee L. Thomas
- Department of Integrative Physiology, University of
Colorado, Boulder, CO, USA
| | - Erika A. Merhroff
- Department of Integrative Physiology, University of
Colorado, Boulder, CO, USA
| | | | | | - Christopher A. Lowry
- Department of Integrative Physiology, Center for
Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder,
Boulder, CO 80309, USA
- Departments of Psychiatry, Neurology, and Physical
Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus,
Aurora, CO 80045, USA
- Rocky Mountain Mental Illness Research Education and
Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center
(RMRVAMC), Aurora, Colorado, 80045, USA
- Military and Veteran Microbiome: Consortium for Research
and Education (MVM-CoRE), Denver, CO 80220, USA
- Senior Fellow, inVIVO Planetary Health, of the Worldwide
Universities Network (WUN), West New York, NJ 07093, USA
| | - Marissa A. Ehringer
- Department of Integrative Physiology, University of
Colorado, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado,
Boulder, CO, USA
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33
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Zhou X, Barkley-Levenson AM, Montilla-Perez P, Telese F, Palmer AA. Functional validation of a finding from a mouse genome-wide association study shows that Azi2 influences the acute locomotor stimulant response to methamphetamine. GENES, BRAIN, AND BEHAVIOR 2021; 20:e12760. [PMID: 34173327 DOI: 10.1111/gbb.12760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022]
Abstract
In a previous genome-wide association study (GWAS) using outbred Carworth Farms White (CFW) mice, we identified a locus that influenced the stimulant response to methamphetamine and colocalized with an eQTL for Azi2. Based on those findings, we hypothesized that heritable differences in Azi2 expression were causally related to the differential response to methamphetamine. To test that hypothesis, we created a mutant Azi2 allele on an inbred C57BL/6J background. The mutant allele enhanced the locomotor response to methamphetamine. However, the GWAS had suggested that lower Azi2 would decrease the locomotor response to methamphetamine. We also sought to explore the mechanism by which Azi2 influenced methamphetamine sensitivity. A recent publication reported that the 3'UTR of Azi2 mRNA downregulates the expression of Slc6a3, which encodes the dopamine transporter, which is a key target of methamphetamine. We evaluated the relationship between Azi2, Azi2 3'UTR and Slc6a3 expression in the ventral tegmental area of wildtype, mutant Azi2 heterozygotes and mutant Azi2 homozygotes and in a new cohort of outbred CFW mice where both allele mapped in our prior GWAS were segregating. We did not observe any correlation between Azi2 and Slc6a3 in either cohort. However, RNA sequencing confirmed that the Azi2 mutation altered Azi2 expression and also revealed a number of potentially important genes and pathways that were regulated by Azi2, including the metabotropic glutamate receptor group III pathway and nicotinic acetylcholine receptor signaling pathway. Our results support a role for Azi2 in methamphetamine sensitivity; however, the exact mechanism does not appear to involve regulation of Slc6a3.
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Affiliation(s)
- Xinzhu Zhou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | | | | | - Francesca Telese
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
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34
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Borrelli KN, Yao EJ, Yen WW, Phadke RA, Ruan QT, Chen MM, Kelliher JC, Langan CR, Scotellaro JL, Babbs RK, Beierle JC, Logan RW, Johnson WE, Wachman EM, Cruz-Martín A, Bryant CD. Sex Differences in Behavioral and Brainstem Transcriptomic Neuroadaptations following Neonatal Opioid Exposure in Outbred Mice. eNeuro 2021; 8:ENEURO.0143-21.2021. [PMID: 34479978 PMCID: PMC8454922 DOI: 10.1523/eneuro.0143-21.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/02/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
The opioid epidemic led to an increase in the number of neonatal opioid withdrawal syndrome (NOWS) cases in infants born to opioid-dependent mothers. Hallmark features of NOWS include weight loss, severe irritability, respiratory problems, and sleep fragmentation. Mouse models provide an opportunity to identify brain mechanisms that contribute to NOWS. Neonatal outbred Swiss Webster Cartworth Farms White (CFW) mice were administered morphine (15 mg/kg, s.c.) twice daily from postnatal day 1 (P1) to P14, an approximation of the third trimester of human gestation. Female and male mice underwent behavioral testing on P7 and P14 to determine the impact of opioid exposure on anxiety and pain sensitivity. Ultrasonic vocalizations (USVs) and daily body weights were also recorded. Brainstems containing pons and medulla were collected during morphine withdrawal on P14 for RNA sequencing. Morphine induced weight loss from P2 to P14, which persisted during adolescence (P21) and adulthood (P50). USVs markedly increased at P7 in females, emerging earlier than males. On P7 and P14, both morphine-exposed female and male mice displayed hyperalgesia on the hot plate and tail-flick assays, with females showing greater hyperalgesia than males. Morphine-exposed mice exhibited increased anxiety-like behavior in the open-field arena on P21. Transcriptome analysis of the brainstem, an area implicated in opioid withdrawal and NOWS, identified pathways enriched for noradrenergic signaling in females and males. We also found sex-specific pathways related to mitochondrial function and neurodevelopment in females and circadian entrainment in males. Sex-specific transcriptomic neuroadaptations implicate unique neurobiological mechanisms underlying NOWS-like behaviors.
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Affiliation(s)
- Kristyn N Borrelli
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
- Graduate Program for Neuroscience, Boston University, Boston, Massachusetts 02118
- Transformative Training Program in Addiction Science, Boston University, Boston, Massachusetts 02118
- NIGMS Training Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Emily J Yao
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - William W Yen
- Neurobiology Section, Department of Biology, Boston University, Boston, Massachusetts 02215
| | - Rhushikesh A Phadke
- Neurobiology Section, Department of Biology, Boston University, Boston, Massachusetts 02215
- Molecular Biology, Cell Biology, and Biochemistry (MCBB), Boston University, Boston, Massachusetts 02215
| | - Qiu T Ruan
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
- Transformative Training Program in Addiction Science, Boston University, Boston, Massachusetts 02118
- NIGMS Training Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Melanie M Chen
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Julia C Kelliher
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Carly R Langan
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Julia L Scotellaro
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
- Undergraduate Research Opportunity Program, Boston University, Boston, Massachusetts 02118
| | - Richard K Babbs
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Jacob C Beierle
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
- Transformative Training Program in Addiction Science, Boston University, Boston, Massachusetts 02118
- NIGMS Training Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Ryan W Logan
- Laboratory of Sleep, Rhythms, and Addiction, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts 02118
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, Maine 04609
| | - William Evan Johnson
- Department of Medicine, Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Elisha M Wachman
- Department of Pediatrics, Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts 02118
| | - Alberto Cruz-Martín
- Neurobiology Section, Department of Biology, Boston University, Boston, Massachusetts 02215
| | - Camron D Bryant
- Laboratory of Addiction Genetics, Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, Massachusetts 02118
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Thomas MH, Gui Y, Garcia P, Karout M, Gomez Ramos B, Jaeger C, Michelucci A, Gaigneaux A, Kollmus H, Centeno A, Schughart K, Balling R, Mittelbronn M, Nadeau JH, Sauter T, Williams RW, Sinkkonen L, Buttini M. Quantitative trait locus mapping identifies a locus linked to striatal dopamine and points to collagen IV alpha-6 chain as a novel regulator of striatal axonal branching in mice. GENES BRAIN AND BEHAVIOR 2021; 20:e12769. [PMID: 34453370 DOI: 10.1111/gbb.12769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022]
Abstract
Dopaminergic neurons (DA neurons) are controlled by multiple factors, many involved in neurological disease. Parkinson's disease motor symptoms are caused by the demise of nigral DA neurons, leading to loss of striatal dopamine (DA). Here, we measured DA concentration in the dorsal striatum of 32 members of Collaborative Cross (CC) family and their eight founder strains. Striatal DA varied greatly in founders, and differences were highly heritable in the inbred CC progeny. We identified a locus, containing 164 genes, linked to DA concentration in the dorsal striatum on chromosome X. We used RNAseq profiling of the ventral midbrain of two founders with substantial difference in striatal DA-C56BL/6 J and A/J-to highlight potential protein-coding candidates modulating this trait. Among the five differentially expressed genes within the locus, we found that the gene coding for the collagen IV alpha 6 chain (Col4a6) was expressed nine times less in A/J than in C57BL/6J. Using single cell RNA-seq data from developing human midbrain, we found that COL4A6 is highly expressed in radial glia-like cells and neuronal progenitors, indicating a role in neuronal development. Collagen IV alpha-6 chain (COL4A6) controls axogenesis in simple model organisms. Consistent with these findings, A/J mice had less striatal axonal branching than C57BL/6J mice. We tentatively conclude that DA concentration and axonal branching in dorsal striatum are modulated by COL4A6, possibly during development. Our study shows that genetic mapping based on an easily measured Central Nervous System (CNS) trait, using the CC population, combined with follow-up observations, can parse heritability of such a trait, and nominate novel functions for commonly expressed proteins.
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Affiliation(s)
- Mélanie H Thomas
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg
| | - Yujuan Gui
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg.,National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
| | - Mona Karout
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg
| | - Borja Gomez Ramos
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Christian Jaeger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg
| | - Alessandro Michelucci
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Neuro-Immunology Group, Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Anthoula Gaigneaux
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Arthur Centeno
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,University of Veterinary Medicine Hannover, Hannover, Germany.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg.,Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg.,National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg.,Neuro-Immunology Group, Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, Washington, USA.,Maine Medical Center Research Institute, Scarborough, Maine, USA
| | - Thomas Sauter
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg
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36
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In Search of Species-Specific SNPs in a Non-Model Animal (European Bison ( Bison bonasus))-Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data. Animals (Basel) 2021; 11:ani11082226. [PMID: 34438684 PMCID: PMC8388393 DOI: 10.3390/ani11082226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/07/2021] [Accepted: 07/24/2021] [Indexed: 11/17/2022] Open
Abstract
The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.
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Baud A, Casale FP, Barkley-Levenson AM, Farhadi N, Montillot C, Yalcin B, Nicod J, Palmer AA, Stegle O. Dissecting indirect genetic effects from peers in laboratory mice. Genome Biol 2021; 22:216. [PMID: 34311762 PMCID: PMC8311926 DOI: 10.1186/s13059-021-02415-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The phenotype of an individual can be affected not only by the individual's own genotypes, known as direct genetic effects (DGE), but also by genotypes of interacting partners, indirect genetic effects (IGE). IGE have been detected using polygenic models in multiple species, including laboratory mice and humans. However, the underlying mechanisms remain largely unknown. Genome-wide association studies of IGE (igeGWAS) can point to IGE genes, but have not yet been applied to non-familial IGE arising from "peers" and affecting biomedical phenotypes. In addition, the extent to which igeGWAS will identify loci not identified by dgeGWAS remains an open question. Finally, findings from igeGWAS have not been confirmed by experimental manipulation. RESULTS We leverage a dataset of 170 behavioral, physiological, and morphological phenotypes measured in 1812 genetically heterogeneous laboratory mice to study IGE arising between same-sex, adult, unrelated mice housed in the same cage. We develop and apply methods for igeGWAS in this context and identify 24 significant IGE loci for 17 phenotypes (FDR < 10%). We observe no overlap between IGE loci and DGE loci for the same phenotype, which is consistent with the moderate genetic correlations between DGE and IGE for the same phenotype estimated using polygenic models. Finally, we fine-map seven significant IGE loci to individual genes and find supportive evidence in an experiment with a knockout model that Epha4 gives rise to IGE on stress-coping strategy and wound healing. CONCLUSIONS Our results demonstrate the potential for igeGWAS to identify IGE genes and shed light into the mechanisms of peer influence.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
- Current Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- Microsoft Research New England, Cambridge, MA USA
| | | | - Nilgoun Farhadi
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
| | - Charlotte Montillot
- INSERM U1231 GAD Laboratory, University Bourgogne Franche-Comté, 21070 Dijon, France
| | - Binnaz Yalcin
- INSERM U1231 GAD Laboratory, University Bourgogne Franche-Comté, 21070 Dijon, France
| | - Jerome Nicod
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Current Address: The Francis Crick Institute, London, UK
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, 69120 Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
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38
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Li S, Cao W, Zhou S, Ma M, Zhang W, Li F, Li C. Expression of Cntn1 is regulated by stress and associated with anxiety and depression phenotypes. Brain Behav Immun 2021; 95:142-153. [PMID: 33737174 DOI: 10.1016/j.bbi.2021.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
In recent years, our understanding of neural circuits associated with depression has increased. Although inherited factors are known to influence individual differences in the risk for this disorder, it has been difficult to identify specific genes that moderate circuit functions affecting depression. Genome-wide association studies have identified genetic variants of Cntn1 that are linked to major depressive disorders. Cntn1, a subset of the neural cell adhesion protein and immunoglobulin supergene family, participates in cell contact formation and axonal growth control and plays a role in degenerative and inflammatory disorders. However, neuronal substrates that mediate Cntn1 action on depression-like phenotypes and involved mechanisms are unclear. Here, we exploited chronic unpredictable stress (CUS) exposure and found that CUS treatment significantly increased hippocampal Cntn1 messenger RNA and protein expression in both mice and rats, but not in the medial prefrontal cortex, which presented a region-specific regulation. Using an adeno-associated virus-based approach to directly overexpress Cntn1 via stereotactic injection, we demonstrated that Cntn1 overexpression in the hippocampus triggered anxiety- and depression-like phenotypes in addition to microglia activation or phagocytosis in the hippocampus, resulting in upregulation of pro-inflammatory cytokine (IL1α, IL6, and Ccl2) mRNA expression and downregulation of anti-inflammatory cytokine (IL4 and CD206) mRNA expression, determined using real-time quantitative PCR, thus impairing hippocampal immature neurons in the dentate gyrus, determined using immunohistochemical staining for doublecortin, a specific marker for immature neurons. Collectively, our results identified Cntn1 as a novel risk gene involved in regulating anxiety and depression via functional actions in the hippocampus that is correlated with microglial activation or phagocytosis and reduced hippocampal immature neurons. These results may provide a better understanding of the pathophysiological mechanisms underlying the risk of depression-related disorders.
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Affiliation(s)
- Songji Li
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410013, China
| | - Wenyu Cao
- Clinical Anatomy & Reproductive Medicine Application Institute, School of Medicine, University of South China, Hengyang, Hunan Province 421001, China
| | - Shifen Zhou
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410013, China
| | - Minhui Ma
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410013, China
| | - Wenjuan Zhang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410013, China
| | - Fang Li
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410013, China
| | - Changqi Li
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan Province 410013, China.
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39
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Cofer EM, Raimundo J, Tadych A, Yamazaki Y, Wong AK, Theesfeld CL, Levine MS, Troyanskaya OG. Modeling transcriptional regulation of model species with deep learning. Genome Res 2021; 31:1097-1105. [PMID: 33888512 PMCID: PMC8168591 DOI: 10.1101/gr.266171.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022]
Abstract
To enable large-scale analyses of transcription regulation in model species, we developed DeepArk, a set of deep learning models of the cis-regulatory activities for four widely studied species: Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, and Mus musculus DeepArk accurately predicts the presence of thousands of different context-specific regulatory features, including chromatin states, histone marks, and transcription factors. In vivo studies show that DeepArk can predict the regulatory impact of any genomic variant (including rare or not previously observed) and enables the regulatory annotation of understudied model species.
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Affiliation(s)
- Evan M Cofer
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.,Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - João Raimundo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Alicja Tadych
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Yuji Yamazaki
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.,Yutaka Seino Distinguished Center for Diabetes Research, Kansai Electric Power Medical Research Institute, Kobe, 650-0047, Japan
| | - Aaron K Wong
- Flatiron Institute, Simons Foundation, New York, New York 10010, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Michael S Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.,Flatiron Institute, Simons Foundation, New York, New York 10010, USA.,Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA
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40
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Bitaraf Sani M, Zare Harofte J, Banabazi MH, Esmaeilkhanian S, Shafei Naderi A, Salim N, Teimoori A, Bitaraf A, Zadehrahmani M, Burger PA, Landi V, Silawi M, Taghipour Sheshdeh A, Faghihi MA. Genomic prediction for growth using a low-density SNP panel in dromedary camels. Sci Rep 2021; 11:7675. [PMID: 33828208 PMCID: PMC8027435 DOI: 10.1038/s41598-021-87296-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/26/2021] [Indexed: 11/29/2022] Open
Abstract
For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
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Affiliation(s)
- Morteza Bitaraf Sani
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran.
| | - Javad Zare Harofte
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), 3146618361, Karaj, Iran
| | - Saeid Esmaeilkhanian
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education and Extension Organization (AREEO), 3146618361, Karaj, Iran
| | - Ali Shafei Naderi
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | - Nader Salim
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, 8916713449, Yazd, Iran
| | - Abbas Teimoori
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, 8916713449, Yazd, Iran
| | - Ahmad Bitaraf
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | | | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, 1160, Vienna, Austria
| | - Vincenzo Landi
- Departement of Veterinary Medicine, Università Di Bari "Aldo Moro", Bari, Italy
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran
| | | | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran.,Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, 33136, USA
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41
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Zhang Q, Yi GY. Marginal analysis of bivariate mixed responses with measurement error and misclassification. Stat Methods Med Res 2021; 30:1155-1186. [PMID: 33635738 DOI: 10.1177/0962280220983587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Bivariate responses with mixed continuous and binary variables arise commonly in applications such as clinical trials and genetic studies. Statistical methods based on jointly modeling continuous and binary variables have been available. However, such methods ignore the effects of response mismeasurement, a ubiquitous feature in applications. It has been well studied that in many settings, ignorance of mismeasurement in variables usually results in biased estimation. In this paper, we consider the setting with a bivariate outcome vector which contains a continuous component and a binary component both subject to mismeasurement. We propose estimating equation approaches to handle measurement error in the continuous response and misclassification in the binary response simultaneously. The proposed estimators are consistent and robust to certain model misspecification, provided regularity conditions. Extensive simulation studies confirm that the proposed methods successfully correct the biases resulting from the error-in-variables under various settings. The proposed methods are applied to analyze the outbred Carworth Farms White mice data arising from a genome-wide association study.
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Affiliation(s)
- Qihuang Zhang
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Grace Y Yi
- Department of Statistics and Actuarial Sciences and Department of Computer Science, University of Western Ontario, London, ON, Canada
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42
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Zhang Q, Yi GY. Genetic association studies with bivariate mixed responses subject to measurement error and misclassification. Stat Med 2020; 39:3700-3719. [PMID: 32914420 DOI: 10.1002/sim.8688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 04/12/2020] [Accepted: 06/13/2020] [Indexed: 01/01/2023]
Abstract
In genetic association studies, mixed effects models have been widely used in detecting the pleiotropy effects which occur when one gene affects multiple phenotype traits. In particular, bivariate mixed effects models are useful for describing the association of a gene with a continuous trait and a binary trait. However, such models are inadequate to feature the data with response mismeasurement, a characteristic that is often overlooked. It has been well studied that in univariate settings, ignorance of mismeasurement in variables usually results in biased estimation. In this paper, we consider the setting with a bivariate outcome vector which contains a continuous component and a binary component both subject to mismeasurement. We propose an induced likelihood approach and an EM algorithm method to handle measurement error in continuous response and misclassification in binary response simultaneously. Simulation studies confirm that the proposed methods successfully remove the bias induced from the response mismeasurement.
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Affiliation(s)
- Qihuang Zhang
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Ontario, N2L3G1, Canada
| | - Grace Y Yi
- Department of Statistical and Actuarial Sciences, Department of Computer Science, University of Western Ontario, London, Ontario, Canada, N6A 5B7
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43
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Hillis DA, Yadgary L, Weinstock GM, Pardo-Manuel de Villena F, Pomp D, Fowler AS, Xu S, Chan F, Garland T. Genetic Basis of Aerobically Supported Voluntary Exercise: Results from a Selection Experiment with House Mice. Genetics 2020; 216:781-804. [PMID: 32978270 PMCID: PMC7648575 DOI: 10.1534/genetics.120.303668] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
The biological basis of exercise behavior is increasingly relevant for maintaining healthy lifestyles. Various quantitative genetic studies and selection experiments have conclusively demonstrated substantial heritability for exercise behavior in both humans and laboratory rodents. In the "High Runner" selection experiment, four replicate lines of Mus domesticus were bred for high voluntary wheel running (HR), along with four nonselected control (C) lines. After 61 generations, the genomes of 79 mice (9-10 from each line) were fully sequenced and single nucleotide polymorphisms (SNPs) were identified. We used nested ANOVA with MIVQUE estimation and other approaches to compare allele frequencies between the HR and C lines for both SNPs and haplotypes. Approximately 61 genomic regions, across all somatic chromosomes, showed evidence of differentiation; 12 of these regions were differentiated by all methods of analysis. Gene function was inferred largely using Panther gene ontology terms and KO phenotypes associated with genes of interest. Some of the differentiated genes are known to be associated with behavior/motivational systems and/or athletic ability, including Sorl1, Dach1, and Cdh10 Sorl1 is a sorting protein associated with cholinergic neuron morphology, vascular wound healing, and metabolism. Dach1 is associated with limb bud development and neural differentiation. Cdh10 is a calcium ion binding protein associated with phrenic neurons. Overall, these results indicate that selective breeding for high voluntary exercise has resulted in changes in allele frequencies for multiple genes associated with both motivation and ability for endurance exercise, providing candidate genes that may explain phenotypic changes observed in previous studies.
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Affiliation(s)
- David A Hillis
- Genetics, Genomics, and Bioinformatics Graduate Program, University of California, Riverside, California 92521
| | - Liran Yadgary
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina 27599
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032
| | | | - Daniel Pomp
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina 27599
| | - Alexandra S Fowler
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California 92521
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Frank Chan
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California 92521
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44
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Hsiao K, Noble C, Pitman W, Yadav N, Kumar S, Keele GR, Terceros A, Kanke M, Conniff T, Cheleuitte-Nieves C, Tolwani R, Sethupathy P, Rajasethupathy P. A Thalamic Orphan Receptor Drives Variability in Short-Term Memory. Cell 2020; 183:522-536.e19. [PMID: 32997977 DOI: 10.1016/j.cell.2020.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 06/09/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022]
Abstract
Working memory is a form of short-term memory that involves maintaining and updating task-relevant information toward goal-directed pursuits. Classical models posit persistent activity in prefrontal cortex (PFC) as a primary neural correlate, but emerging views suggest additional mechanisms may exist. We screened ∼200 genetically diverse mice on a working memory task and identified a genetic locus on chromosome 5 that contributes to a substantial proportion (17%) of the phenotypic variance. Within the locus, we identified a gene encoding an orphan G-protein-coupled receptor, Gpr12, which is sufficient to drive substantial and bidirectional changes in working memory. Molecular, cellular, and imaging studies revealed that Gpr12 enables high thalamus-PFC synchrony to support memory maintenance and choice accuracy. These findings identify an orphan receptor as a potent modifier of short-term memory and supplement classical PFC-based models with an emerging thalamus-centric framework for the mechanistic understanding of working memory.
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Affiliation(s)
- Kuangfu Hsiao
- Laboratory of Neural Dynamics & Cognition, The Rockefeller University, New York, NY 10065, USA
| | - Chelsea Noble
- Laboratory of Neural Dynamics & Cognition, The Rockefeller University, New York, NY 10065, USA
| | - Wendy Pitman
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Nakul Yadav
- Laboratory of Neural Dynamics & Cognition, The Rockefeller University, New York, NY 10065, USA
| | - Suraj Kumar
- Laboratory of Neural Dynamics & Cognition, The Rockefeller University, New York, NY 10065, USA
| | | | - Andrea Terceros
- Laboratory of Neural Dynamics & Cognition, The Rockefeller University, New York, NY 10065, USA
| | - Matt Kanke
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Tara Conniff
- Laboratory of Neural Dynamics & Cognition, The Rockefeller University, New York, NY 10065, USA
| | | | - Ravi Tolwani
- Comparative Bioscience Center, The Rockefeller University, New York, NY 10065, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
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45
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Parker CC, Lusk R, Saba LM. Alcohol Sensitivity as an Endophenotype of Alcohol Use Disorder: Exploring Its Translational Utility between Rodents and Humans. Brain Sci 2020; 10:E725. [PMID: 33066036 PMCID: PMC7600833 DOI: 10.3390/brainsci10100725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 12/21/2022] Open
Abstract
Alcohol use disorder (AUD) is a complex, chronic, relapsing disorder with multiple interacting genetic and environmental influences. Numerous studies have verified the influence of genetics on AUD, yet the underlying biological pathways remain unknown. One strategy to interrogate complex diseases is the use of endophenotypes, which deconstruct current diagnostic categories into component traits that may be more amenable to genetic research. In this review, we explore how an endophenotype such as sensitivity to alcohol can be used in conjunction with rodent models to provide mechanistic insights into AUD. We evaluate three alcohol sensitivity endophenotypes (stimulation, intoxication, and aversion) for their translatability across human and rodent research by examining the underlying neurobiology and its relationship to consumption and AUD. We show examples in which results gleaned from rodents are successfully integrated with information from human studies to gain insight in the genetic underpinnings of AUD and AUD-related endophenotypes. Finally, we identify areas for future translational research that could greatly expand our knowledge of the biological and molecular aspects of the transition to AUD with the broad hope of finding better ways to treat this devastating disorder.
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Affiliation(s)
- Clarissa C. Parker
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, VT 05753, USA
| | - Ryan Lusk
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Laura M. Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
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46
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Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Bimschleger H, Garcia Martinez A, George T, Gileta AF, Han W, Horvath A, Hughson A, Ishiwari K, King CP, Lamparelli A, Versaggi CL, Martin C, St Pierre CL, Tripi JA, Wang T, Chen H, Flagel SB, Meyer P, Richards J, Robinson TE, Palmer AA, Solberg Woods LC. Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. Obesity (Silver Spring) 2020; 28:1964-1973. [PMID: 32860487 PMCID: PMC7511439 DOI: 10.1002/oby.22927] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Obesity is influenced by genetic and environmental factors. Despite the success of human genome-wide association studies, the specific genes that confer obesity remain largely unknown. The objective of this study was to use outbred rats to identify the genetic loci underlying obesity and related morphometric and metabolic traits. METHODS This study measured obesity-relevant traits, including body weight, body length, BMI, fasting glucose, and retroperitoneal, epididymal, and parametrial fat pad weight in 3,173 male and female adult N/NIH heterogeneous stock (HS) rats across three institutions, providing data for the largest rat genome-wide association study to date. Genetic loci were identified using a linear mixed model to account for the complex family relationships of the HS and using covariates to account for differences among the three phenotyping centers. RESULTS This study identified 32 independent loci, several of which contained only a single gene (e.g., Epha5, Nrg1, Klhl14) or obvious candidate genes (e.g., Adcy3, Prlhr). There were strong phenotypic and genetic correlations among obesity-related traits, and there was extensive pleiotropy at individual loci. CONCLUSIONS This study demonstrates the utility of HS rats for investigating the genetics of obesity-related traits across institutions and identify several candidate genes for future functional testing.
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Affiliation(s)
- Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Katie Holl
- Human and Molecular Genetic Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Hannah Bimschleger
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Tony George
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | - Alexander F Gileta
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Wenyan Han
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Aidan Horvath
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Alesa Hughson
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Keita Ishiwari
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | | | | | | | - Connor Martin
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | | | - Jordan A Tripi
- Department of Psychology, University at Buffalo, Buffalo, New York, USA
| | - Tengfei Wang
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Hao Chen
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Shelly B Flagel
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul Meyer
- Department of Psychology, University at Buffalo, Buffalo, New York, USA
| | - Jerry Richards
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | - Terry E Robinson
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Wang Y, Bu L, Cao X, Qu H, Zhang C, Ren J, Huang Z, Zhao Y, Luo C, Hu X, Shu D, Li N. Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line. Front Genet 2020; 11:894. [PMID: 33033489 PMCID: PMC7509424 DOI: 10.3389/fgene.2020.00894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F2 generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F0, F2, F8, and F9 generations of AIL and demonstrate that the population of the F9 generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F2 generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth.
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Affiliation(s)
- Yuzhe Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lina Bu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuemin Cao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hao Qu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chunyuan Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiangli Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhuolin Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Gao J, Lyu Y, Zhang D, Reddi KK, Sun F, Yi J, Liu C, Li H, Yao H, Dai J, Xu F. Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat ( Capra hircus). Front Genet 2020; 11:901. [PMID: 32973871 PMCID: PMC7472782 DOI: 10.3389/fgene.2020.00901] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/21/2020] [Indexed: 12/23/2022] Open
Abstract
The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14-20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion-deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide F ST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.
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Affiliation(s)
- Jun Gao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Yuhua Lyu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Defu Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Kiran Kumar Reddi
- Department of Bioscience Research, College of Dentistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Fengping Sun
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jianzhong Yi
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chengqian Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hong Li
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huijuan Yao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jianjun Dai
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Fuyi Xu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
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49
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Gileta AF, Gao J, Chitre AS, Bimschleger HV, St Pierre CL, Gopalakrishnan S, Palmer AA. Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats. G3 (BETHESDA, MD.) 2020; 10:2195-2205. [PMID: 32398234 PMCID: PMC7341140 DOI: 10.1534/g3.120.401325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 05/01/2020] [Indexed: 02/06/2023]
Abstract
The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.
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Affiliation(s)
- Alexander F Gileta
- Department of Psychiatry
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, 92093
| | | | | | | | | | - Shyam Gopalakrishnan
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, and
| | - Abraham A Palmer
- Department of Psychiatry,
- Natural History Museum of Denmark, University of Copenhagen, 2200 København N, Denmark
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50
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Vanhatalo J, Li Z, Sillanpää MJ. A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data. Bioinformatics 2020; 35:3684-3692. [PMID: 30850830 PMCID: PMC6761969 DOI: 10.1093/bioinformatics/btz164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 12/05/2018] [Accepted: 03/06/2019] [Indexed: 12/22/2022] Open
Abstract
Motivation Recent advances in high dimensional phenotyping bring time as an extra dimension into the phenotypes. This promotes the quantitative trait locus (QTL) studies of function-valued traits such as those related to growth and development. Existing approaches for analyzing functional traits utilize either parametric methods or semi-parametric approaches based on splines and wavelets. However, very limited choices of software tools are currently available for practical implementation of functional QTL mapping and variable selection. Results We propose a Bayesian Gaussian process (GP) approach for functional QTL mapping. We use GPs to model the continuously varying coefficients which describe how the effects of molecular markers on the quantitative trait are changing over time. We use an efficient gradient based algorithm to estimate the tuning parameters of GPs. Notably, the GP approach is directly applicable to the incomplete datasets having even larger than 50% missing data rate (among phenotypes). We further develop a stepwise algorithm to search through the model space in terms of genetic variants, and use a minimal increase of Bayesian posterior probability as a stopping rule to focus on only a small set of putative QTL. We also discuss the connection between GP and penalized B-splines and wavelets. On two simulated and three real datasets, our GP approach demonstrates great flexibility for modeling different types of phenotypic trajectories with low computational cost. The proposed model selection approach finds the most likely QTL reliably in tested datasets. Availability and implementation Software and simulated data are available as a MATLAB package ‘GPQTLmapping’, and they can be downloaded from GitHub (https://github.com/jpvanhat/GPQTLmapping). Real datasets used in case studies are publicly available at QTL Archive. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jarno Vanhatalo
- Department of Mathematics and Statistics and Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Zitong Li
- CSIRO Agriculture & Food, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Mikko J Sillanpää
- Department of Mathematical Sciences, Biocenter Oulu and Infotech Oulu University of Oulu, Oulu FI-90014, Finland
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